B.4. EMBOSS Applications (release R6)

Table B.3. EMBOSS Applications (release R6)
aaindexextractExtract amino acid property data from AAINDEX
abiviewDisplay the trace in an ABI sequencer file
acdcTest an application ACD file
acdprettyCorrectly reformat an application ACD file
acdtableGenerate an HTML table of parameters from an application ACD file
acdtraceTrace processing of an application ACD file (for testing)
acdvalidValidate an application ACD file
aligncopyReads and writes alignments
aligncopypairReads and writes pairs from alignments
antigenicFinds antigenic sites in proteins
backtranambigBack-translate a protein sequence to ambiguous nucleotide sequence
backtranseqBack-translate a protein sequence to a nucleotide sequence
bananaPlot bending and curvature data for B-DNA
biosedReplace or delete sequence sections
btwistedCalculate the twisting in a B-DNA sequence
caiCalculate codon adaptation index
chaosDraw a chaos game representation plot for a nucleotide sequence
chargeDraw a protein charge plot
checktransReports STOP codons and ORF statistics of a protein
chipsCalculates Nc codon usage statistic
cirdnaDraws circular maps of DNA constructs
codcmpCodon usage table comparison
codcopyCopy and reformat a codon usage table
coderetExtract CDS, mRNA and translations from feature tables
compseqCalculate the composition of unique words in sequences
consCreate a consensus sequence from a multiple alignment
consambigCreate an ambiguous consensus sequence from a multiple alignment
cpgplotIdentify and plot CpG islands in nucleotide sequence(s)
cpgreportIdentify and report CpG-rich regions in nucleotide sequence(s)
cuspCreate a codon usage table from nucleotide sequence(s)
cutgextractExtract codon usage tables from CUTG database
cutseqRemoves a section from a sequence
danCalculates nucleic acid melting temperature
dbiblastIndex a BLAST database
dbifastaIndex a fasta file database
dbiflatIndex a flat file database
dbigcgIndex a GCG formatted database
dbxfastaIndex a fasta file database using b+tree indices
dbxflatIndex a flat file database using b+tree indices
dbxgcgIndex a GCG formatted database using b+tree indices
degapseqRemoves non-alphabetic (e.g. gap) characters from sequences
densityDraw a nucleic acid density plot
descseqAlter the name or description of a sequence
diffseqCompare and report features of two similar sequences
digestReports on protein proteolytic enzyme or reagent cleavage sites
distmatCreate a distance matrix from a multiple sequence alignment
dotmatcherDraw a threshold dotplot of two sequences
dotpathDraw a non-overlapping wordmatch dotplot of two sequences
dottupDisplays a wordmatch dotplot of two sequences
dregRegular expression search of nucleotide sequence(s)
edialignLocal multiple alignment of sequences
einvertedFinds inverted repeats in nucleotide sequences
embossdataFind and retrieve EMBOSS data files
embossversionReports the current EMBOSS version number
emmaMultiple sequence alignment (ClustalW wrapper)
emowseSearch protein sequences by digest fragment molecular weight
entretRetrieves sequence entries from flatfile databases and files
epestfindFinds PEST motifs as potential proteolytic cleavage sites
eprimer3Picks PCR primers and hybridization oligos
equicktandemFinds tandem repeats in nucleotide sequences
est2genomeAlign EST sequences to genomic DNA sequence
etandemFinds tandem repeats in a nucleotide sequence
extractalignExtract regions from a sequence alignment
extractfeatExtract features from sequence(s)
extractseqExtract regions from a sequence
featcopyReads and writes a feature table
featreportReads and writes a feature table
findkmCalculate and plot enzyme reaction data
freakGenerate residue/base frequency table or plot
fuzznucSearch for patterns in nucleotide sequences
fuzzproSearch for patterns in protein sequences
fuzztranSearch for patterns in protein sequences (translated)
garnierPredicts protein secondary structure using GOR method
geeceeCalculate fractional GC content of nucleic acid sequences
getorfFinds and extracts open reading frames (ORFs)
helixturnhelixIdentify nucleic acid-binding motifs in protein sequences
hmomentCalculate and plot hydrophobic moment for protein sequence(s)
iepCalculate the isoelectric point of proteins
infoalignDisplay basic information about a multiple sequence alignment
infobaseReturn information on a given nucleotide base
inforesidueReturn information on a given amino acid residue
infoseqDisplay basic information about sequences
isochorePlots isochores in DNA sequences
jaspextractExtract data from JASPAR
jaspscanScans DNA sequences for transcription factors
lindnaDraws linear maps of DNA constructs
listorWrite a list file of the logical OR of two sets of sequences
makenucseqCreate random nucleotide sequences
makeprotseqCreate random protein sequences
marscanFinds matrix/scaffold recognition (MRS) signatures in DNA sequences
maskambignucMasks all ambiguity characters in nucleotide sequences with N
maskambigprotMasks all ambiguity characters in protein sequences with X
maskfeatWrite a sequence with masked features
maskseqWrite a sequence with masked regions
matcherWaterman-Eggert local alignment of two sequences
megamergerMerge two large overlapping DNA sequences
mergerMerge two overlapping sequences
msbarMutate a sequence
mwcontamFind weights common to multiple molecular weights files
mwfilterFilter noisy data from molecular weights file
needleNeedleman-Wunsch global alignment of two sequences
needleallMany-to-many pairwise alignments of two sequence sets
newcpgreportIdentify CpG islands in nucleotide sequence(s)
newcpgseekIdentify and report CpG-rich regions in nucleotide sequence(s)
newseqCreate a sequence file from a typed-in sequence
nohtmlRemove mark-up (e.g. HTML tags) from an ASCII text file
noreturnRemove carriage return from ASCII files
nospaceRemove all whitespace from an ASCII text file
notabReplace tabs with spaces in an ASCII text file
notseqWrite to file a subset of an input stream of sequences
nthseqWrite to file a single sequence from an input stream of sequences
nthseqsetReads and writes (returns) one set of sequences from many
octanolDraw a White-Wimley protein hydropathy plot
oddcompIdentify proteins with specified sequence word composition
palindromeFinds inverted repeats in nucleotide sequence(s)
pasteseqInsert one sequence into another
patmatdbSearches protein sequences with a sequence motif
patmatmotifsScan a protein sequence with motifs from the PROSITE database
pepcoilPredicts coiled coil regions in protein sequences
pepinfoPlot amino acid properties of a protein sequence in parallel
pepnetDraw a helical net for a protein sequence
pepstatsCalculates statistics of protein properties
pepwheelDraw a helical wheel diagram for a protein sequence
pepwindowDraw a hydropathy plot for a protein sequence
pepwindowallDraw Kyte-Doolittle hydropathy plot for a protein alignment
plotconPlot conservation of a sequence alignment
plotorfPlot potential open reading frames in a nucleotide sequence
polydotDraw dotplots for all-against-all comparison of a sequence set
pregRegular expression search of protein sequence(s)
prettyplotDraw a sequence alignment with pretty formatting
prettyseqWrite a nucleotide sequence and its translation to file
primersearchSearch DNA sequences for matches with primer pairs
printsextractExtract data from PRINTS database for use by pscan
profitScan one or more sequences with a simple frequency matrix
prophecyCreate frequency matrix or profile from a multiple alignment
prophetScan one or more sequences with a Gribskov or Henikoff profile
prosextractProcesses the PROSITE motif database for use by patmatmotifs
pscanScans protein sequence(s) with fingerprints from the PRINTS database
psiphiCalculates phi and psi torsion angles from protein coordinates
rebaseextractProcess the REBASE database for use by restriction enzyme applications
recoderFind restriction sites to remove (mutate) with no translation change
redataRetrieve information from REBASE restriction enzyme database
remapDisplay restriction enzyme binding sites in a nucleotide sequence
restoverFind restriction enzymes producing a specific overhang
restrictReport restriction enzyme cleavage sites in a nucleotide sequence
revseqReverse and complement a nucleotide sequence
seealsoFinds programs with similar function to a specified program
seqmatchallAll-against-all word comparison of a sequence set
seqretReads and writes (returns) sequences
seqretsetallReads and writes (returns) many sets of sequences
seqretsplitReads sequences and writes them to individual files
showalignDisplay a multiple sequence alignment in pretty format
showdbDisplays information on configured databases
showfeatDisplay features of a sequence in pretty format
showorfDisplay a nucleotide sequence and translation in pretty format
showpepDisplays protein sequences with features in pretty format
showseqDisplays sequences with features in pretty format
shuffleseqShuffles a set of sequences maintaining composition
sigcleaveReports on signal cleavage sites in a protein sequence
silentFind restriction sites to insert (mutate) with no translation change
sirnaFinds siRNA duplexes in mRNA
sixpackDisplay a DNA sequence with 6-frame translation and ORFs
sizeseqSort sequences by size
skipredundantRemove redundant sequences from an input set
skipseqReads and writes (returns) sequences, skipping first few
splitsourceSplit sequence(s) into original source sequences
splitterSplit sequence(s) into smaller sequences
stretcherNeedleman-Wunsch rapid global alignment of two sequences
stssearchSearch a DNA database for matches with a set of STS primers
supermatcherCalculate approximate local pair-wise alignments of larger sequences
sycoDraw synonymous codon usage statistic plot for a nucleotide sequence
tcodeIdentify protein-coding regions using Fickett TESTCODE statistic
textsearchSearch the textual description of sequence(s)
tfextractProcess TRANSFAC transcription factor database for use by tfscan
tfmDisplays full documentation for an application
tfscanIdentify transcription factor binding sites in DNA sequences
tmapPredict and plot transmembrane segments in protein sequences
tranalignGenerate an alignment of nucleic coding regions from aligned proteins
transeqTranslate nucleic acid sequences
trimestRemove poly-A tails from nucleotide sequences
trimseqRemove unwanted characters from start and end of sequence(s)
trimspaceRemove extra whitespace from an ASCII text file
twofeatFinds neighbouring pairs of features in sequence(s)
unionConcatenate multiple sequences into a single sequence
vectorstripRemoves vectors from the ends of nucleotide sequence(s)
waterSmith-Waterman local alignment of sequences
whichdbSearch all sequence databases for an entry and retrieve it
wobblePlot third base position variability in a nucleotide sequence
wordcountCount and extract unique words in molecular sequence(s)
wordfinderMatch large sequences against one or more other sequences
wordmatchFinds regions of identity (exact matches) of two sequences
wossnameFinds programs by keywords in their short description
yankAdd a sequence reference (a full USA) to a list file